Liquid NMA: A surprisingly realistic model for hydrogen bonding motifs in proteins

Chemical Physics Letters

Volumn 414, Issue 1-3, 2005, Pages 210-214

  Whitfield, Troy W ^a   Martyna, Glenn J ^a   Allison, Susan ^b   Bates, Simon P ^b   Crain, Jason ^a,b  

^a IBM T J WATSON RESEARCH CENTER   (United States)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; HYDROGEN BONDS; MOLECULAR DYNAMICS; OXYGEN; TOPOLOGY;

INTERCHAIN ASSOCIATIONS; LIQUID N-METHYLACETAMIDE; METHYL HYDROGEN ATOMS;

PROTEINS;

EID: 28844501708     PISSN: 00092614     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cplett.2005.08.073     Document Type: Article

References (29)

1. M.L. Huggins Chem. Rev. 32 1943 195
2. G.C. Pimentel, and A.L. McClellan The Hydrogen Bond 1960 W.H. Freeman and Co. San Francisco
3. R. Taylor, and O. Kennard J. Am. Chem. Soc. 104 1982 5063
4. Z.S. Derewenda, L. Lee, and U. Derewenda J. Mol. Biol. 252 1995 248
5. G.F. Fabiola, S. Krishnaswamy, V. Nagaragan, and V. Pattabhi Acta Cryst. D 53 1997 316
6. R.L. Baldwin Biophys. Chem. 101-102 2002 203
7. R.A. Vergenz, I. Yazji, C. Whittington, J. Daw, and K.T. Tran J. Am. Chem. Soc. 125 2003 12318
8. K. Manikandan, and S. Ramakumar Proteins 56 2004 768
9. R. Zhang, H. Li, Y. Lei, and S. Han J. Phys. Chem. B 108 2004 12596
10. M. Mottamal, and T. Lazaridis Biochemistry 44 2005 1607
11. T.W. Whitfield, L. Bu, and J.E. Straub Physica A 305 2002 157
12. K.B. Wibreg, and D.J. Rush J. Org. Chem. 67 2002 826
13. S.K. Gregurick, G.M. Chaban, and R.B. Gerber J. Phys. Chem. A 106 2002 8696
14. Y.A. Mantz, H. Gerard, R. Iftimie, and G.J. Martyna J. Am. Chem. Soc. 126 2004 4080
15. A.D. Becke Phys. Rev. A 38 1988 3098
16. C. Lee, W. Yang, and R.G. Parr Phys. Rev. B 37 1988 785
17. R. Car, and M. Parrinello Phys. Rev. Lett. 55 1985 2471
18. A.D. MacKerell Jr. J. Phys. Chem. B 102 1998 3586
19. L. Dougan J. Chem. Phys. 121 2004 6456
20. G.J. Martyna, M.L. Klein, and M. Tuckerman J. Chem. Phys. 97 1992 2635
21. G.J. Martyna, M.E. Tuckerman, D.J. Tobias, and M.L. Klein Mol. Phys. 87 1996 1117
22. D.J. Tobias, M.L. Klein, and G.J. Martyna J. Chem. Phys. 101 1994 4177
23. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen J. Comput. Phys. 23 1977 327
24. H.C. Andersen J. Comput. Phys. 52 1983 24
25. M.E. Tuckerman, and M. Parrinello J. Chem. Phys. 101 1994 1302
26. M.E. Tuckerman, and M. Parrinello J. Chem. Phys. 101 1994 1316
27. J. Hutter, M.E. Tuckerman, and M. Parrinello J. Chem. Phys. 102 1995 859
28. W. Kohn, Y. Meir, and D.E. Makarov Phys. Rev. Lett. 80 1998 4153
29. T.W. Whitfield, G.J. Martyna, S. Allison, S.P. Bates, H. Vass, J. Crain J. Phys. Chem. B (in press).